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Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 30, 2019 - Issue 3
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Research Article

Multigene barcoding and phylogeny of selected Engraulidae species

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Pages 548-555 | Received 06 Sep 2018, Accepted 22 Dec 2018, Published online: 20 Mar 2019

References

  • Bamaniya DC, Pavan-Kumar A, Gireesh-Babu P, Sharma N, Reang D, Krishna G, Lakra WS. 2016. DNA barcoding of marine ornamental fishes from India. Mitochondrial DNA A DNA Mapp Seq Anal. 27:3093–3097.
  • Bineesh KK, Gopalakrishnan A, Akhilesh KV, Sajeela KA, Abdussamad EM, Pillai NGK, Basheer VS, Jena JK, Ward RD. 2017. DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery. Mitochondrial DNA Part A. 28:458–472.
  • Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. Plos One. 13:e0198109.
  • Bloom DD, Lovejoy NR. 2012. Molecular phylogenetic reveals a pattern of biome conservatism in New World anchovies (family Engraulidae). J Evol Biol. 25:701–715.
  • CMFRI. 2018. Fish catch estimates. Accessed 2018 Oct 12. http://www.cmfri.org.in/fish-catch-estimates
  • Conflitti M, Shields GF, Currie DC. 2012. A “complex” problem: delimiting sibling species boundaries in black flies (Diptera: Simuliidae). Can Entomol. 144:323–336.
  • Daniel N, Pavan-Kumar A, Kiruba-Sankar Praveenraj A, Kathirvelpandian A, Damroy S, Chaudhari A. 2018. First record of whitebarred goby Amblygobius phalaena (Valenciennes, 1837) from Indian waters. Indian J Fish. 65:116–121.
  • DeSalle R, Egan MG, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci. 360:1905–1916.
  • Egan JP, Bloom DD, Kuo CH, Hammer MP, Tongnunui P, Iglésias SP, Sheaves M, Grudpan C, Simons AM. 2018. Phylogenetic analysis of trophic niche evolution reveals a latitudinal herbivory gradient in Clupeoidei (herrings, anchovies, and allies). Mol Phylogenet Evol. 124:151–161.
  • Eschmeyer WN, Fricke R, van der Laan R. 2018. Catalog of fishes: Genera, Species, References. (http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp). Electronic version accessed 2018 Aug 05.
  • FAO. 2018. The state of world fisheries and aquaculture 2018. Rome (Italy): FAO.
  • Gopi KC, Mishra SS. 2015. Diversity of marine fishes of India. In: Venkataraman K, Sivaperuman C, editors. Marine faunal diversity in India. Taxonomy, ecology and conservation. San Diego: Academic Press; p. 171–193.
  • Grande L, Nelson GJ. 1985. Interrelationships of fossil and recent anchovies (Teleostei: Engrauloidea) and description of a new species from the Miocene of Cyprus. Am Mus Novit. 2826:1–16.
  • Grande L. 1985. Recent and fossil clupeomorph fishes with materials for revision of the subgroups of clupeoids. Bull Am Mus Nat His. 181:231–372.
  • Hata H, Motomura H. 2017a. A new species of anchovy, Encrasicholina auster (Clupeiformes: Engraulidae) from Fiji, southwestern Pacific Ocean. New Zeal J Zool. 44:122–128.
  • Hata H, Motomura H. 2017b. Validity of Encrasicholina pseudoheteroloba (Hardenberg 1933) and redescription of Encrasicholina heteroloba (Rüppell 1837), a senior synonym of Encrasicholina devisi (Whitley 1940) (Clupeiformes: Engraulidae). Ichthyol Res. 64:18–28.
  • Hata H, Motomura H. 2015. A new species of anchovy, Encrasicholina macrocephala (Clupeiformes: Engraulidae), from the northwestern Indian Ocean. Zootaxa. 3941:117–124.
  • Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc Biol Sci. 270:313–321.
  • Hildebrand SF. 1963. Family Engraulidae. Mem Sears Found Mar Res. 1:152–249.
  • Hubert N, Meyer CP, Bruggemann HJ, Guérin F, Komeno RJL, Espiau B, Causse R, Williams JT, Planes S. 2012. Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis. PLoS One. 7:e28987.
  • Huelsenbeck JP, Ronquist F. 2003. MR BAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
  • Imran Z, Yamao M. 2014. Factors contributing to the decline of the anchovy fisheries in Krueng Raya Bay, Aceh, Indonesia. Ann Trop Res. 36:22–43.
  • Kannuchamy N, Pavan-Kumar A, Venkateshwarlu G, Gireesh-Babu P, Lakra WS. 2016. Mislabelling in Indian seafood: an investigation using DNA barcoding. Food Control. 59:196–200.
  • Krück NC, Tibbetts IR, Ward RD, Johnson JW, Loh WKW, Ovenden JR. 2013. Multi-gene barcoding to discriminate sibling species within a morphologically difficult fish genus (Sillago). Fish Res. 143:39–46.
  • Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 33:1870–1874.
  • Lakra WS, Verma MS, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh KV, Ward RD, Hebert PDN. 2011. DNA barcoding Indian marine fishes. Mol Ecol Resour. 11:60–71.
  • Lavoue ÂS, Bertrand JAM, Wang H-Y, Chen W-J, Ho H-C, Motomura H, Hata H, Sado T, Miya M. 2017. Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific. PLoS One. 12:e0181329.
  • Lavoue S, Miya M, Nishida M. 2010. Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes. Mol Phylogenet Evol. 56:480–485.
  • Li C, Orti G. 2007. Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences. Mol Phylogent Evol. 44:386–398.
  • Liu J, Jiang J, Song S, Tornabene L, Chabarria R, Naylor GJP, Li C. 2017. Multilocus DNA barcoding - species identification with multilocus data. Sci Rep. 7:16601.
  • Mwale M, Dalton DL, Jansen R, De Bruyn M, Pietersen D, Mokgokong PS, Kotzé A. 2017. Forensic application of DNA barcoding for identification of illegally traded African pangolin scales. Genome. 60:272–284.
  • Nelson SJ, Grande TC, Wilson MVH. 2016. Fishes of the world. NJ: John Wiley & Sons.
  • Pavan-Kumar A, Kumar R, Pitale P, Shen KN, Borsa P. 2018. Neotrygon indica sp. nov., the Indian Ocean blue-spotted maskray (Myliobatoidei, Dasyatidae). C R Biologies. 341:120–130.
  • Pavan-Kumar A, Gireesh-Babu P, Suresh Babu PP, Jaiswar AK, Prasad KP, Chaudhari A, Raje SG, Chakraborty SK, Krishna G, Lakra WS. 2015. DNA barcoding of elasmobranchs from Indian coast and its reliability in delineating geographically widespread specimens. Mitochondrial DNA. 26:92–100.
  • Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25:1253–1256.
  • Rach J, Desalle R, Sarkar IN, Schierwater B, Hadrys H. 2008. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc Biol Sci. 275:237–247.
  • Ratnasingham S, Hebert PDN. 2007. BOLD: the barcode of life data system (http://www.barcodinglife.org)). Mol Ecol Notes. 7:355–364.
  • Ratnasingham S, Hebert PDN. 2013. A DNA-based registry for all animal species: the barcode index number (BIN) system. Plos One. 8:e66213.
  • Sadurudeen N, Pavan-Kumar A, Gireesh-Babu P, Jaiswar AK, Chaudhari A, Krishna G, Lakra WS. 2017. DNA barcoding of selected Perciformes (Infra Class: Teleostei) fishes from Indian coast. Indian J Biotechnol. 16:315–321.
  • Shekhar MS, Natarajan M, Vinaya KK. 2011. PCR-RFLP and sequence analysis of 12S and 16S rRNA mitochondrial genes of Grey mullets from East coast of India. Indian J Geomarine Sci. 40:529–534.
  • Supongpan M, Chamchang C, Boongerd S, Laowapong A. 2000. Technical report on the anchovy fisheries in the Gulf of Thailand. FAO/FISHCODE Project GCP/INT/648/NOR: Field report F-6 Suppl. (En). Rome: FAO.
  • Swofford DL. 2003. PAUP: phylogenetic analysis using parsimony (and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA. Markov model. Appl Math Lett. 7:19–23.
  • Valdez-Moreno M, Vásquez-Yeomans L, Elías-Gutiérrez M, Ivanova NV, Hebert PDN. 2010. Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management. Mar Freshwater Res. 61:655–671.
  • van Velzen R, Weitschek E, Felici G, Bakker FT. 2012. DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One. 7:e30490.
  • Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR. 2005. Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool. 2:5.
  • Viswambharan D, Pavan-Kumar A, Singh DP, Jaiswar AK, Chakraborty SK, Nair JR, Lakra WS. 2015. DNA barcoding of gobiid fishes (Perciformes, Gobioidei). Mitochondrial DNA. 26:15–19.
  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert P. 2005. DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci. 360:1847–1857.
  • Whitehead PJP. 1972. A synopsis of the clupeoid fishes of India. Mar Biol Ass India. 14:160–256.
  • Whitehead PJP, Nelson GJ, Wongratana T. 1988. Clupeoid fishes of the World (Suborder Clupeoidei): an annotated and illustrated catalogue of the herrings, sardines, pilchards, sprats, shads, anchovies and wolf herrings. Part 2. Engraulididae. FAO Fisheries Synopsis. 125:305–579.
  • Wong EHK, Shivji MS, Hanner RH. 2009. Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour. 9:243–256.
  • Wongratana T. 1980. Systematics of Clupeoid fishes of the Indo-Pacific Region. Ph.D. thesis. Faculty of Science, University of London, 432 pp.
  • Wongratana T. 1983. Diagnosis of 24 new species and proposal of a new name for a species of Indo-Pacific clupeoid fishes. Japan J Ichthyol. 29:385–407.
  • Wongratana T. 1987. Two new species of anchovies of genus Stolephorus (Engraulidae), with a key to species of Engraulis, Encrasicholina, and Stolephorus. Am Mus Novit. 2867:1–8.
  • Wongratana T, Munroe TA, Nizinski MS. 1995. Bony Fishes. Order Clupeiformes: Engraulidae, Anchovies. Rome: FAO. Retrieved from http://www.fao.org/3/a-x2401e/x2401e24.pdf.
  • Xia X, Xie Z. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 92:371–373.
  • Yamamoto S, Masuda R, Sato Y, Sato T, Araki H, Kondoh M, Minamoto T, Miya M. 2017. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep. 7:40368.
  • Zhang JB, Hanner R. 2011. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol. 39:31–42.

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